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Microbial Community Structure and Seasonal Variations in Mudflat Sediments of Sansha Bay, China - 987

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Microbial Community Structure and Seasonal Variations in Mudflat Sediments of Sansha Bay, China - 987 Yang et al.: Microbial community structure and seasonal variations in mudflat sediments of Sansha Bay, China - 987 - MICROBIAL COMMUNITY STRUCTURE AND SEASONAL VARIATIONS IN MUDFLAT SEDIMENTS OF SANSHA BAY, CHINA YANG, Z.1 – WANG, Y. Z.1 – WU, Z. C.1 – REN, L. R.1 – XIONG, C. J.2 – MA, Y.1* 1Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College of Jimei University, Xiamen 361021, China 2College of Foreign Language, Hunan University, Changsha 410006, China *Corresponding author e-mail: [email protected]; phone: +86-1896-5423-006; fax: +86-0592-6181-476 (Received 13th Jul 2019; accepted 25th Nov 2019) Abstract. Illumina high-throughput sequencing was applied to study the microbial community structure and seasonal variations in the mudflat sediments of Sansha Bay, China. Significant seasonal differences of microbial communities were observed, and pH, total P, total N, and organic carbon concentration were important factors affecting the microbial communities. A total of 52 bacterial phyla were detected in the sediments, dominated by γ-Proteobacteria (27.78%), δ-Proteobacteria (20.16%) and Bacteroidetes (10.58%). A total of 717 bacterial genera were detected, and among the top 100 genera with the highest abundances, 48 genera changed significantly (p <0.05) with seasons. The microbial community structure in summer was significantly different from others, and the environmental factors driving the changes were mainly temperature, organic carbon and total N concentration. The bacteria with higher abundances in summer were mainly attached bacteria, thermophilic bacteria, anaerobic bacteria, and those involved in carbon and nitrogen cycling, while in other seasons, those with higher abundances were mainly aerobic bacteria, which could adapt to low temperatures and are involved in the degradation of cellulose and chitosan. However, the physicochemical indexes didn’t change significantly, which indicated that the bacterial communities are more sensitive and can serve as a good sentinel for environmental changes. Keywords: Illumina high-throughput sequencing, bacterial genetic diversity, seasonal changes, intertidal sediments, physiochemical characteristics, Sansha Bay Introduction Traditionally, marine environmental quality is assessed by physical-chemical and biological indexes, such as dissolved oxygen (DO), chemical oxygen demand (COD), nitrogen (N), phosphorus (P), heavy metal, persistent pollutant, and so on (Arsad et al., 2012). However, such static indexes have difficulties characterizing the structure and function of the marine ecosystem (Viswanathan et al., 2010). At present, most of the biological indicators used to characterize ecosystem structure and function are large animals, plants or benthos (Cabana et al., 2013; Hannah, 2015; Wang et al., 2018), or some microscopically visible single-celled organisms, such as diatoms and cyanobacteria (Daby, 2006). Nevertheless, when the impact of the disturbance has caused obvious changes in these biological indicators, the time of early warning is long gone. Microorganisms are one of the most important components of the intertidal zones of mudflat ecosystems, and are involved in nutrient cycling, energy flow, organic matter degradation, and pollutant removal. Microbial communities are sensitive to environmental variation, which makes them ideal biological indicators for environmental pollution and ecosystem changes (Sun et al., 2012). Total coliforms, APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH 18(1):987-1000. http://www.aloki.hu ● ISSN 1589 1623 (Print) ● ISSN1785 0037 (Online) DOI: http://dx.doi.org/10.15666/aeer/1801_9871000 © 2020, ALÖKI Kft., Budapest, Hungary Yang et al.: Microbial community structure and seasonal variations in mudflat sediments of Sansha Bay, China - 988 - fecal coliforms (Escherichia coli) and enterococci have been commonly used as indicators to assess the microbiological safety of water resources (Lage and Bondoso, 2011). Previous studies also showed that there was a positive and strong association of total phosphorous, total nitrogen, and ammonium-nitrogen contents with micro- eukaryotes and Gram-positive bacteria (Zhao et al., 2010), and several metals are also strongly associated with microbial community composition (Cao et al., 2006). Although microorganisms are more sensitive to environmental changes and are better indicators for environmental quality, they have not been adopted as environmental quality indexes yet due to our poor understanding of them and the difficulty of detection. The emergence of molecular biological technique, especially the high- throughput sequencing, has provided us important opportunity for fully and deeply understand environmental microbes because of the high data throughput (103–106 sequences per sample), high accuracy and low cost. This technique enables us to identify the dominant and rare populations within a community simultaneously, thus it could reveal a significantly greater level of microbial diversity than conventional molecular tools (Binladen et al., 2007; Caporaso and Gordon, 2011). Sansha Bay is a typical enclosed bay, which is located on the southeastern coast of Ningde City, Fujian Province, and includes Dongwuyang, Guanjingyang, and Sanduao. The streams and rivers from the eight surrounding cities, with a basin area of 8,700 km2, flow into this harbor, containing the domestic sewage of over 2 million people (Tang et al., 2018). In recent years, due to the high discharge of domestic sewage and industrial wastewater as well as the large inflow of residual breeding bait, the mudflat environment has been subjected to substantial pollution. The main goals of the study are to investigate the community structure and seasonal variations of organisms in mudflat sediments of Sansha Bay, and their relationship to physicochemical indexes. The results present here will provide microbial parameters for assessing the environment quality, and to lay a foundation for further illumination of the ecological functions of microorganisms in mudflat sediments. Methods Sample collection and physiochemical index analysis The study was performed in the Northern Yantian port of Sansha Bay (Fig. A1). The total area was about 2.6 acre, at an east longitude from 119.7975 to 119.7986 and a northern latitude from 26.8411 to 30.8422. The study area was divided into four plots, and sediment samples of each plot were collected on 10 October, 2014 (autumn), 2 January, 2015 (winter), 6 April 2015 (spring), and 2 July 2015 (summer). The sediments of the surface layer (top 3-5 cm) were removed and about 200 g subsurface sediments from three different sites within the same plot were collected and mixed as one sample, resulting in a total of 16 samples in four batches. The samples were termed as Oct-P1 to Oct-P4, Jan-P1 to Jan-P4, Apr-P1 to Apr-P4, Jul-P1 to Jul-P4, according to sampling time and sampling plots. All the 16 sediment samples were used for the determination of the physicochemical indices, 10 g sediments of each sample were freeze-dried in a lyophilizer (Labconco, Kansas City, MO, USA). The following parameters were analyzed, and each sample was measured twice. Total nitrogen (TN) was determined via the Kjeldahl method (Bradstreet, 1954) and total phosphorus (TP) via the ammonium molybdate spectrophotometric method (GB11894-89, China; Huang, APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH 18(1):987-1000. http://www.aloki.hu ● ISSN 1589 1623 (Print) ● ISSN1785 0037 (Online) DOI: http://dx.doi.org/10.15666/aeer/1801_9871000 © 2020, ALÖKI Kft., Budapest, Hungary Yang et al.: Microbial community structure and seasonal variations in mudflat sediments of Sansha Bay, China - 989 - 2000). Organic matter contents (OrgC and OrgS) were determined via a Vario Max CNS analyzer (Elementar, Hanau, Germany). For the determination of pH, sediment and water were mixed at a ratio of 1:5 (W/V). Water temperature (Tm) was measured on the site. DNA extraction, PCR amplification, and Illumina sequencing For DNA extraction with the PowerSoil DNA Isolation Kit (MOBIO-Laboratories, USA), we used 0.25 g of the sediment samples. The V4 variable region in the bacterial 16S rRNA gene was amplified with the primer pair 515F (5'- GTG CCA GCM GCC GCG GTA A-3') and 806R (5'- GGA CTA CHV GGG TWT CTA AT-3'). The PCR products of the different samples were mixed with equimolar concentration and sent to the Majorbio Co. Ltd. (Shanghai) for paired-end sequencing through the Illumina Miseq platform. Bioinformatic analysis Post-processing of the Illumina sequence reads included quality control and clustering of the operational taxonomic unit (OTU) with 97% sequence identity. The QIIME was applied to collect the OTUs for sequence clustering, the chimeras were removed, and OTU abundance was defined. The RDP Bayesian classifier was applied to conduct taxonomic analyses on OUT-representative sequences with 97% similarity level; the classification was identified in the Silva database (Release128 http://www.arb-silva.de), and the community composition of each sample was analyzed at each classification level, including phylum, class, order, family, genus, and OTU. Mothur software was used to analyze alpha diversity. Community diversity was estimated by Shannon (Magurran, 1988) and Simpson (Simpson, 1949) indices. The total number of species in each sample was estimated with Chao1 and Ace. Phylogenetic diversity (PD) whole tree was used to analyze the relationships among observed species. Sampling coverage was used to evaluate whether
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